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https://www.readbyqxmd.com/read/28212542/two-stage-genome-wide-association-study-identifies-a-novel-susceptibility-locus-associated-with-melanoma
#1
Katherine J Ransohoff, Wenting Wu, Hyunje G Cho, Harvind C Chahal, Yuan Lin, Hong-Ji Dai, Christopher I Amos, Jeffrey E Lee, Jean Y Tang, David A Hinds, Jiali Han, Qingyi Wei, Kavita Y Sarin
Genome-wide association studies have identified 21 susceptibility loci associated with melanoma. These loci implicate genes affecting pigmentation, nevus count, telomere maintenance, and DNA repair in melanoma risk. Here, we report the results of a two-stage genome-wide association study of melanoma. The stage 1 discovery phase consisted of 4,842 self-reported melanoma cases and 286,565 controls of European ancestry from the 23andMe research cohort and the stage 2 replication phase consisted of 1,804 melanoma cases and 1,026 controls from the University of Texas M...
February 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28212531/msmb-gene-rs10993994-polymorphism-increases-the-risk-of-prostate-cancer
#2
Tao Peng, Lifeng Zhang, Lijie Zhu, Yuan-Yuan Mi
Genome-wide association studies (GWASs) identified microseminoprotein-β (MSMB) gene rs10993994 polymorphism was significantly associated with prostate cancer (PC) risk. However, the association between MSMB gene rs10993994 polymorphism and PC risk remains controversial. Therefore, we performed a systematic review and meta-analysis by searching in the databases of PubMed, and Embase. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by using fixed-effect or random-effect models. A total of 11 publications containing 13 case-control studies for rs10993994 polymorphism were included in our analysis...
February 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28212402/graph-gpa-a-graphical-model-for-prioritizing-gwas-results-and-investigating-pleiotropic-architecture
#3
Dongjun Chung, Hang J Kim, Hongyu Zhao
Genome-wide association studies (GWAS) have identified tens of thousands of genetic variants associated with hundreds of phenotypes and diseases, which have provided clinical and medical benefits to patients with novel biomarkers and therapeutic targets. However, identification of risk variants associated with complex diseases remains challenging as they are often affected by many genetic variants with small or moderate effects. There has been accumulating evidence suggesting that different complex traits share common risk basis, namely pleiotropy...
February 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28212376/the-legionella-pneumophila-genome-evolved-to-accommodate-multiple-regulatory-mechanisms-controlled-by-the-csra-system
#4
Tobias Sahr, Christophe Rusniok, Francis Impens, Giulia Oliva, Odile Sismeiro, Jean-Yves Coppée, Carmen Buchrieser
The carbon storage regulator protein CsrA regulates cellular processes post-transcriptionally by binding to target-RNAs altering translation efficiency and/or their stability. Here we identified and analyzed the direct targets of CsrA in the human pathogen Legionella pneumophila. Genome wide transcriptome, proteome and RNA-Co-immunoprecipitaion followed by deep sequencing of a wild type and a csrA mutant strain identified 479 RNAs with potential CsrA interaction sites located in the untranslated and/or coding regions of mRNAs or of known non-coding sRNAs...
February 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28212332/type-1-diabetes-candidate-genes-linked-to-pancreatic-islet-cell-inflammation-and-beta-cell-apoptosis
#5
REVIEW
Joachim Størling, Flemming Pociot
Type 1 diabetes (T1D) is a chronic immune-mediated disease resulting from the selective destruction of the insulin-producing pancreatic islet β-cells. Susceptibility to the disease is the result of complex interactions between environmental and genetic risk factors. Genome-wide association studies (GWAS) have identified more than 50 genetic regions that affect the risk of developing T1D. Most of these susceptibility loci, however, harbor several genes, and the causal variant(s) and gene(s) for most of the loci remain to be established...
February 16, 2017: Genes
https://www.readbyqxmd.com/read/28212331/analysis-of-epidermal-growth-factor-receptor-related-gene-expression-changes-in-a-cellular-and-animal-model-of-parkinson-s-disease
#6
In-Su Kim, Sushruta Koppula, Shin-Young Park, Dong-Kug Choi
We employed transcriptome analysis of epidermal growth factor receptor related gene expression changes in cellular and animal models of Parkinson's disease (PD). We used a well-known Parkinsonian toxin 1-methyl-4-phenylpyridine (MPP⁺) to induce neuronal apoptosis in the human neuroblastoma SH-SY5Y cell line. The MPP⁺-treatment of SH-SY5Y cells was capable of inducing neuro-apoptosis, but it remains unclear what kinds of transcriptional genes are affected by MPP⁺ toxicity. Therefore the pathways that were significantly perturbed in MPP⁺ treated human neuroblastoma SH-SY5Y cells were identified based on genome-wide gene expression data at two time points (24 and 48 h)...
February 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28212312/genome-wide-prediction-of-dna-methylation-using-dna-composition-and-sequence-complexity-in-human
#7
Chengchao Wu, Shixin Yao, Xinghao Li, Chujia Chen, Xuehai Hu
DNA methylation plays a significant role in transcriptional regulation by repressing activity. Change of the DNA methylation level is an important factor affecting the expression of target genes and downstream phenotypes. Because current experimental technologies can only assay a small proportion of CpG sites in the human genome, it is urgent to develop reliable computational models for predicting genome-wide DNA methylation. Here, we proposed a novel algorithm that accurately extracted sequence complexity features (seven features) and developed a support-vector-machine-based prediction model with integration of the reported DNA composition features (trinucleotide frequency and GC content, 65 features) by utilizing the methylation profiles of embryonic stem cells in human...
February 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28212192/genetic-control-of-erythropoiesis
#8
Laxminath Tumburu, Swee Lay Thein
PURPOSE OF REVIEW: The discovery of several genetic variants associated with erythroid traits and subsequent elucidation of their functional mechanisms are exemplars of the power of the new genetic and genomic technology. The present review highlights findings from recent genetic studies related to the control of erythropoiesis and dyserythropoiesis, and fetal hemoglobin, an erythroid-related trait. RECENT FINDINGS: Identification of the genetic modulators of erythropoiesis involved two approaches: genome-wide association studies (GWASs) using single nucleotide polymorphism (SNP) arrays that revealed the common genetic variants associated with erythroid phenotypes (hemoglobin, red cell count, MCV, MCH) and fetal hemoglobin; and massive parallel sequencing such as whole genome sequencing (WGS) and whole exome sequencing (WES) that led to the discovery of the rarer variants (GFI1B, SBDS, RPS19, PKLR, EPO, EPOR, KLF1, GATA1)...
February 15, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28211990/homozygous-mutation-in-prune1-in-an-oji-cree-male-with-a-complex-neurological-phenotype
#9
Gregory Costain, Andrea Shugar, Pradeep Krishnan, Saadet Mahmutoglu, Suzanne Laughlin, Peter Kannu
The PRUNE1 gene encodes a member of the phosphoesterases (DHH) protein superfamily that is highly expressed in the human fetal brain and involved in the regulation of cell migration. Homozygous or compound heterozygous PRUNE1 mutations were recently identified in five individuals with brain malformations from four families. We present a case of a 2-year-old male with a complex neurological phenotype and abnormalities on brain MRI. Re-annotation of clinical whole-exome sequencing data revealed a homozygous likely pathogenic variant in PRUNE1 (c...
March 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28211912/dna-methylation-map-in-circulating-leukocytes-mirrors-subcutaneous-adipose-tissue-methylation-pattern-a-genome-wide-analysis-from-non-obese-and-obese-patients
#10
A B Crujeiras, A Diaz-Lagares, J Sandoval, F I Milagro, S Navas-Carretero, M C Carreira, A Gomez, D Hervas, M P Monteiro, F F Casanueva, M Esteller, J A Martinez
The characterization of the epigenetic changes within the obesity-related adipose tissue will provide new insights to understand this metabolic disorder, but adipose tissue is not easy to sample in population-based studies. We aimed to evaluate the capacity of circulating leukocytes to reflect the adipose tissue-specific DNA methylation status of obesity susceptibility. DNA samples isolated from subcutaneous adipose tissue and circulating leukocytes were hybridized in the Infinium HumanMethylation 450 BeadChip...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211892/high-throughput-in-situ-cell-electroporation-microsystem-for-parallel-delivery-of-single-guide-rnas-into-mammalian-cells
#11
Shengtai Bian, Yicen Zhou, Yawei Hu, Jing Cheng, Xiaofang Chen, Youchun Xu, Peng Liu
Arrayed genetic screens mediated by the CRISPR/Cas9 technology with single guide RNA (sgRNA) libraries demand a high-throughput platform capable of transfecting diverse cell types at a high efficiency in a genome-wide scale for detection and analysis of sophisticated cellular phenotypes. Here we developed a high-throughput in situ cell electroporation (HiCEP) microsystem which leveraged the superhydrophobic feature of the microwell array to achieve individually controlled conditions in each microwell and coupled an interdigital electrode array chip with the microwells in a modular-based scheme for highly efficient delivery of exogenous molecules into cells...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211812/recent-progress-in-alzheimer-s-disease-research-part-2-genetics-and-epidemiology
#12
Morgan Robinson, Brenda Y Lee, Francis T Hane
This is the second part of a three-part review series reviewing the most important advances in Alzheimer's disease (AD) research since 2010. This review covers the latest research on genetics and epidemiology. Epidemiological and genetic studies are revealing important insights into the etiology of, and factors that contribute to AD, as well as areas of priority for research into mechanisms and interventions. The widespread adoption of genome wide association studies has provided compelling evidence of the genetic complexity of AD with genes associated with such diverse physiological function as immunity and lipid metabolism being implicated in AD pathogenesis...
February 16, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28211678/high-throughput-screening-of-sulfated-proteins-by-using-a-genome-wide-proteome-microarray-and-protein-tyrosine-sulfation-system
#13
Bo-Yu Huang, Po-Chung Chen, Bo-Han Chen, Chen-Chu Wang, Hsuan-Fu Liu, Yi-Zao Chen, Chien-Sheng Chen, Yuh-Shyong Yang
Protein tyrosine sulfation (PTS) is a widespread posttranslational modification that induces intercellular and extracellular responses by regulating protein-protein interactions and enzymes activities. Although PTS affects numerous physiological and pathological processes, only a small fraction of the total predicted sulfated proteins has been identified to date. Here, we localized the potential sulfation sites of Escherichia coli proteins on a proteome microarray by using a 3'-phosphoadenosine 5'-phosphosulfate (PAPS) synthase-coupled tyrosylprotein sulfotransferase (TPST) catalysis system that involves in situ PAPS generation and TPST catalysis...
February 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28211582/what-can-genome-wide-association-studies-tell-us-about-the-evolutionary-forces-maintaining-genetic-variation-for-quantitative-traits
#14
REVIEW
Emily B Josephs, John R Stinchcombe, Stephen I Wright
I. II. III. IV. V. References SUMMARY: Understanding the evolutionary forces that shape genetic variation within species has long been a goal of evolutionary biology. Integrating data for the genetic architecture of traits from genome-wide association mapping studies (GWAS) along with the development of new population genetic methods for identifying selection in sequence data may allow us to evaluate the roles of mutation-selection balance and balancing selection in shaping genetic variation at various scales...
February 17, 2017: New Phytologist
https://www.readbyqxmd.com/read/28211519/palindromic-amplification-of-the-erbb2-oncogene-in-primary-her2-positive-breast-tumors
#15
Michael Marotta, Taku Onodera, Jeffrey Johnson, G Thomas Budd, Takaaki Watanabe, Xiaojiang Cui, Armando E Giuliano, Atsushi Niida, Hisashi Tanaka
Oncogene amplification confers a growth advantage to tumor cells for clonal expansion. There are several, recurrently amplified oncogenes throughout the human genome. However, it remains unclear whether this recurrent amplification is solely a manifestation of increased fitness resulting from random amplification mechanisms, or if a genomic locus-specific amplification mechanism plays a role. Here we show that the ERBB2 oncogene at 17q12 is susceptible to palindromic gene amplification, a mechanism characterized by the inverted (palindromic) duplication of genomic segments, in HER2-positive breast tumors...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211474/dissection-of-genomic-features-and-variations-of-three-pathotypes-of-puccinia-striiformis-through-whole-genome-sequencing
#16
Kanti Kiran, Hukam C Rawal, Himanshu Dubey, R Jaswal, Subhash C Bhardwaj, P Prasad, Dharam Pal, B N Devanna, Tilak R Sharma
Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici, is one of the important diseases of wheat. We used NGS technologies to generate a draft genome sequence of two highly virulent (46S 119 and 31) and a least virulent (K) pathotypes of P. striiformis from the Indian subcontinent. We generated ~24,000-32,000 sequence contigs (N50;7.4-9.2 kb), which accounted for ~86X-105X sequence depth coverage with an estimated genome size of these pathotypes ranging from 66.2-70.2 Mb. A genome-wide analysis revealed that pathotype 46S 119 might be highly evolved among the three pathotypes in terms of year of detection and prevalence...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211118/transcriptional-and-cell-cycle-alterations-mark-aging-of-primary-human-adipose-derived-stem-cells
#17
Xiaoyin Shan, Cleresa Roberts, Eun Ji Kim, Ariana Brenner, Gregory Grant, Ivona Percec
Adult stem cells play a critical role in the maintenance of tissue homeostasis and prevention of aging. While the regenerative potential of stem cells with low cellular turnover, such as adipose-derived stem cells (ASC), is increasingly recognized, the study of chronological aging in ASCs is technically difficult, and remains poorly understood. Here, we employ our model of chronological aging in primary human ASCs to examine genome-wide transcriptional networks. We demonstrate first that the transcriptome of aging ASCs is distinctly more stable than that of age-matched fibroblasts, and further, that age-dependent modifications in cell cycle progression and translation initiation specifically characterize aging ASCs in conjunction with increased nascent protein synthesis and a distinctly shortened G1 phase...
February 17, 2017: Stem Cells
https://www.readbyqxmd.com/read/28209808/galactosylation-of-iga1-is-associated-with-common-variation-in-c1galt1
#18
Daniel P Gale, Karen Molyneux, David Wimbury, Patricia Higgins, Adam P Levine, Ben Caplin, Anna Ferlin, Peiran Yin, Christopher P Nelson, Horia Stanescu, Nilesh J Samani, Robert Kleta, Xueqing Yu, Jonathan Barratt
IgA nephropathy (IgAN), an important cause of kidney failure, is characterized by glomerular IgA deposition and is associated with changes in O-glycosylation of the IgA1 molecule. Here, we sought to identify genetic factors contributing to levels of galactose-deficient IgA1 (Gd-IgA1) in white and Chinese populations. Gd-IgA1 levels were elevated in IgAN patients compared with ethnically matched healthy subjects and correlated with evidence of disease progression. White patients with IgAN exhibited significantly higher Gd-IgA1 levels than did Chinese patients...
February 16, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28209632/high-resolution-profiling-of-nmd-targets-in-yeast-reveals-translational-fidelity-as-a-basis-for-substrate-selection
#19
Alper Celik, Richard Baker, Feng He, Allan Jacobson
Nonsense-mediated mRNA decay (NMD) plays an important role in eukaryotic gene expression yet the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we re-evaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. Our new RNA-Seq analyses confirm previous results of microarray studies, but also uncover hundreds of new NMD-regulated transcripts that had escaped previous detection, including many intron-containing pre-mRNAs and several non-coding RNAs...
February 16, 2017: RNA
https://www.readbyqxmd.com/read/28209587/genome-surgery-using-cas9-ribonucleoproteins-for-the-treatment-of-age-related-macular-degeneration
#20
Kyoungmi Kim, Sung Wook Park, Jin Hyoung Kim, Seung Hwan Lee, Daesik Kim, Taeyoung Koo, Kwang-Eun Kim, Jeong Hun Kim, Jin-Soo Kim
RNA-guided genome surgery using CRISPR-Cas9 nucleases has shown promise for the treatment of diverse genetic diseases. Yet, the potential of such nucleases for therapeutic applications in nongenetic diseases is largely unexplored. Here, we focus on age-related macular degeneration (AMD), a leading cause of blindness in adults, which is associated with retinal overexpression of, rather than mutations in, the VEGFA gene. Subretinal injection of preassembled, Vegfa gene-specific Cas9 ribonucleoproteins (RNPs) into the adult mouse eye gave rise to mutagenesis at the target site in the retinal pigment epithelium...
February 16, 2017: Genome Research
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